I just like to comment that its a very long winded process and It would be better if it would be done right up front in the initial server setup process instead of after.
Also I'm not to sure about the update process and what affect that will have on the system. ie is it going to be OK to do a normal apt-get update in the future and what happens when there is a dist update not to mention updating ispconfig and that every time we will have go in and manually adjust several files.
I agree. I wonder if there is a way to compile just the packages you need, not all the packages within the Apache2 source.
For instance, when I recompile Apache2 I also add quota to WEBDAV, I don't need everything else.
Also, there is a way you can use apt to use your new packages as a repository. I think I'll add that to the how-to to make the process less error prone.
Then all you would have to do is run 'apt-get upgrade' and it would install all the packages necessary without you having to guess which ones to install.